how to combine two output of RepeatMasker?
1
0
Entering edit mode
6.9 years ago
kk.mahsa ▴ 140

hi

i run homology-based and denovo identification of repeats using Repeatmasker and Repeatmodeler. Now i have two output that i want to combine them to obtain final content of different repetitive elements. how can i do it? anyone can to help me?

RepeatMasker repeats next-gen • 2.8k views
ADD COMMENT
0
Entering edit mode

Please post example input and expected output example

ADD REPLY
0
Entering edit mode

example file is here example

ADD REPLY
1
Entering edit mode
6.9 years ago
ATpoint 83k

You mean getting a kind of consensus list from the two files? If so, merge the files using cat and then use BEDtools merge to get consensus intervals:

cat *.bed | sort -k1,1 -k2,2n | BEDtools merge -i - > consensus.bed
ADD COMMENT
0
Entering edit mode

i have two output files (.out) that some elements between them are shared and some are unique. i want to get one file that give me consensus repetitive elements

ADD REPLY

Login before adding your answer.

Traffic: 1490 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6